[Ontology-editors] histone modifications - process or function?

[Jane Lomax]

Okay, that's what I thought too. I've put the new terms in SF if anyone 
wants to make further comments:

https://sourceforge.net/tracker2/?func=detail&aid=2433533&group_id=36855&atid=440764
https://sourceforge.net/tracker2/?func=detail&aid=2433618&group_id=36855&atid=440764

Jane

David Hill wrote:
> I agree that process would be the most conservative choice.
>
> Midori Harris wrote:
>> Yeah, there are tons in the protein/amino acid modification area. 
>> David and I have just been thinking (hoping?) the f-p links would 
>> help make sense of it all.
>>
>> For the mapping, process sounds reasonable; it's just possible that 
>> something other than the catalytic gp could also be involved in the 
>> modification (yes, I'm hand-waving!).
>> m
>>
>> On Tue, 16 Dec 2008, Jane Lomax wrote:
>>
>>> Hi - I've got a small mapping to do (~50 terms), most of which are 
>>> histone modifications, e.g.
>>>
>>> Histone 2B Acetylation
>>> Histone 2B Acetylation  K5
>>> Histone 2B Acetylation  K12
>>>
>>> We have terms for specific histone modifications in both function 
>>> e.g. 'histone lysine N-acetyltransferase activity (H3-K56 specific)' 
>>> and process e.g. 'histone H3-R17 methylation'.
>>>
>>> So I'm not sure whether to add the new terms for the mapping to 
>>> process or function. I'm leaning towards process.
>>>
>>> And more generally, there are a lot of cases like this where we have 
>>> a chemical reaction that is essentially duplicated in both process 
>>> and function (e.g. phosphorylation v/s kinase). We'll be able to 
>>> make function-process links between these terms soon - so does it 
>>> really matter that we have this duplication?
>>>
>>> Jane
>>>
>>>
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-- 
Dr Jane Lomax
GO Editorial Office
EMBL-EBI
Wellcome Trust Genome Campus
Hinxton
Cambridgeshire, UK
CB10 1SD

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